[Ifeffit] selection of pixels by criteria

[Will Bennett]

Hi all,

I use ImageJ with the ScatterJ and ScatterJn plugins to do this type of analysis of XRF maps.

https://openresearchsoftware.metajnl.com/articles/10.5334/jors.89/

https://onlinelibrary.wiley.com/doi/abs/10.1111/jmi.12187

Cheers,

Will

Dr William W. Bennett

Senior Lecturer
Environmental Futures Research Institute
School of Environment and Science
Griffith University
Gold Coast, Queensland, Australia
M +61 401 186 488
w.bennett at griffith.edu.a<mailto:w.bennett at griffith.edu.au>u

Assistant Professor
Nordcee, Department of Biology
University of Southern Denmark
Odense, Denmark
M +45 8193 8111
wbennett at biology.sdu.dk<mailto:wbennett at biology.sdu.dk>

________________________________
From: Matthew Marcus <mamarcus at lbl.gov>
Sent: Friday, 22 November 2019 6:33 am
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] selection of pixels by criteria

A suggestion: Make a scatterplot available, plotting the pixel-by-pixel values of any two relevant quantities, and make it
possible to define a polygon mask on that scatterplot. That often allows separation of chemically-distinct areas.

Sincerely,
Matthew Marcus

On 11/21/2019 12:26 PM, Matt Newville wrote:
> HI Troy,
>
> Sorry for the late reply -- I think this sort of slipped off my radar screen.
>
>
> On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury <troy.rasbury at stonybrook.edu <mailto:troy.rasbury at stonybrook.edu>> wrote:
>
> I have used larch some for XRF maps. I like the feature for defining ROI's and then looking at the statistics of the data. I have some samples that are an intimate mix of two or more phases and I would like to extract pixels based on a criteria- like high Sr or low Fe, etc, from across a whole map region. I wonder if this feature is available, or would be easy to create on larch?
>
>
> Like you say, this is not currently available in the Mapviewer GUI.  But it's a good suggestion and might be possible to do with a small amount of code.
>
> Would it work for you to say "Make an Area with all pixels where Sr Counts is above some value"?  I think that would be easy to generalize from "Sr Counts" to
> "Ratio of ROI Counts"  (or "analyzed concentration" once I get that done - a work in progress).  If that's right, I think it would be "not hard to add".
>
> --Matt
>
>
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